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<div class="section" id="Introduction-to-atomman:-CIF-conversions">
<h1>Introduction to atomman: CIF conversions<a class="headerlink" href="#Introduction-to-atomman:-CIF-conversions" title="Permalink to this headline">¶</a></h1>
<p><strong>Lucas M. Hale</strong>, <a class="reference external" href="mailto:lucas&#46;hale&#37;&#52;&#48;nist&#46;gov?Subject=ipr-demo">lucas<span>&#46;</span>hale<span>&#64;</span>nist<span>&#46;</span>gov</a>, <em>Materials Science and Engineering Division, NIST</em>.</p>
<p><a class="reference external" href="http://www.nist.gov/public_affairs/disclaimer.cfm">Disclaimers</a></p>
<div class="section" id="1.-Introduction">
<h2>1. Introduction<a class="headerlink" href="#1.-Introduction" title="Permalink to this headline">¶</a></h2>
<p>The Crystallographic Information File (CIF) format is a standard for representing crystallographic information and is used by different crystal databases. Loading CIF files in atomman requires that the <a class="reference external" href="https://github.com/diffpy/diffpy.structure">diffpy.structure</a> package be installed.</p>
<p>Atomman supports loading atomic structures from CIF files but not writing CIF files based on the structures.</p>
<p><strong>Library Imports</strong></p>
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<span></span><span class="c1"># Standard Python libraries</span>
<span class="kn">import</span> <span class="nn">datetime</span>

<span class="c1"># http://www.numpy.org/</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>

<span class="kn">import</span> <span class="nn">atomman</span> <span class="k">as</span> <span class="nn">am</span>
<span class="kn">import</span> <span class="nn">atomman.unitconvert</span> <span class="k">as</span> <span class="nn">uc</span>

<span class="c1"># Show atomman version</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;atomman version =&#39;</span><span class="p">,</span> <span class="n">am</span><span class="o">.</span><span class="n">__version__</span><span class="p">)</span>

<span class="c1"># Show date of Notebook execution</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Notebook executed on&#39;</span><span class="p">,</span> <span class="n">datetime</span><span class="o">.</span><span class="n">date</span><span class="o">.</span><span class="n">today</span><span class="p">())</span>
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atomman version = 1.4.0
Notebook executed on 2021-08-04
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<p>CIF file taken from Crystallography Open Database (COD): <a class="reference external" href="http://www.crystallography.net/">http://www.crystallography.net/</a></p>
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<span class="s2">#$Date: 2016-02-13 21:28:24 +0200 (Sat, 13 Feb 2016) $</span>
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<span class="s2">_atom_site_U_iso_or_equiv</span>
<span class="s2">Ta1 Ta 0 0 0 1 0.0</span>
<span class="s2">&quot;&quot;&quot;</span>
</pre></div>
</div>
</div>
</div>
<div class="section" id="2.-atomman.load(‘cif’)">
<h2>2. atomman.load(‘cif’)<a class="headerlink" href="#2.-atomman.load(‘cif’)" title="Permalink to this headline">¶</a></h2>
<p>Parameters</p>
<ul class="simple">
<li><p><strong>cif</strong> (<em>str or file-like object</em>) The cif content to read.</p></li>
</ul>
<p>Returns</p>
<ul class="simple">
<li><p><strong>system</strong> (<em>atomman.System</em>) An atomman representation of a system.</p></li>
</ul>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="k">try</span><span class="p">:</span>
    <span class="n">cif_system</span> <span class="o">=</span> <span class="n">am</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s1">&#39;cif&#39;</span><span class="p">,</span> <span class="n">cif</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">AssertionError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
    <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;AssertionError:&#39;</span><span class="p">,</span> <span class="n">e</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">cif_system</span><span class="p">)</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">cif_system</span><span class="o">.</span><span class="n">atoms_df</span><span class="p">())</span>
</pre></div>
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</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
avect =  [ 3.303,  0.000,  0.000]
bvect =  [ 0.000,  3.303,  0.000]
cvect =  [ 0.000,  0.000,  3.303]
origin = [ 0.000,  0.000,  0.000]
natoms = 2
natypes = 1
symbols = (&#39;Ta&#39;,)
pbc = [ True  True  True]
per-atom properties = [&#39;atype&#39;, &#39;pos&#39;]
     id |   atype |  pos[0] |  pos[1] |  pos[2]
      0 |       1 |   0.000 |   0.000 |   0.000
      1 |       1 |   1.651 |   1.651 |   1.651
   atype   pos[0]   pos[1]   pos[2]
0      1  0.00000  0.00000  0.00000
1      1  1.65128  1.65128  1.65128
</pre></div></div>
</div>
</div>
</div>


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<li><a class="reference internal" href="#">Introduction to atomman: CIF conversions</a><ul>
<li><a class="reference internal" href="#1.-Introduction">1. Introduction</a></li>
<li><a class="reference internal" href="#2.-atomman.load(‘cif’)">2. atomman.load(‘cif’)</a></li>
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